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Bongino said on X that Saturday was his last day on the job before he would return to "civilian life."
"It's been an incredible year thanks to the leadership and decisiveness of President Trump. It was the honor of a lifetime to work with Director Patel, and to serve you, the American people. See you on the other side," he wrote.
The former FBI deputy director announced in mid-December that he would be leaving his role at the bureau at the start of the new year.
President Donald Trump previously praised Bongino, who assumed office in March, for his work at the FBI.
"Dan did a great job. I think he wants to go back to his show," Trump told reporters.
Bongino spoke publicly about the personal toll of the job during a May appearance on "Fox & Friends," saying he had sacrificed a lot to take the role.
"I gave up everything for this," he said, citing the long hours both he and FBI Director Kash Patel work.
"I stare at these four walls all day in D.C., by myself, divorced from my wife — not divorced, but I mean separated — and it's hard. I mean, we love each other, and it's hard to be apart," he added.
Bongino's departure leaves Andrew Bailey, who was appointed co-deputy director in September 2025, as the bureau's other deputy director.
Comment: Bongino has spent his time since leaving office blocking anyone on X who have the temerity to call him out for how useless he was during his time as FBI deputy director and alienating his own fans. Like Kash Patel, whatever plans he had to help turn around the country was completely neutered once he took the job because the Deep State knows exactly how to control them.